Phylomatic

An online tool to assemble species lists into phylogenies

2009-11-10 changes

The base tree for online phylomatic is now a APG3
derived megatree. The base tree used for the past couple years
had not been updated, and it is time to sync the online phylomatic
with the phylomatic2 database. However, this requires users
adopting some changes: i) I have restricted some of the options
available on this page, ii) The major change is that the
phylomatic2 database uses all lowercase names for taxa in the
database, and so your input trees must be all lowercase (for taxa
to be matched; the terminal name can still contain uppercase
chars). A good editor will be able to `downcase' your input file
in a single action. I apologize for this step if you have got
used to using this resource as is, but for a while I have been
urging users to switch to the desktop phylomatic (included in
phylocom) and the phylomatic2 database. At least you will be able
to access an up-to-date tree this way. Note that the Davies tree
still uses uppercase first characters of taxon names.

API

Added a XML output
option, and the ability to send requests as GET statements, so
phylomatic can be used as a simple web service now.

1. Paste your community list

This `/' delimited format allows the creation of unlimited user-defined structure (see sample). The program reads the string from right to left, matching the taxon at the first position it can in i) the growing user-defined tree, or ii) the `megatree.'